The Azzurri took the lead in the 33rd minute when Juventus center back Giorgio Chiellini found the net.
Although Eder's vicious free kick was parried by Spain goalkeeper David de Gea, Italy midfielder Emanuele Giaccherini - following the rebound - pounced on the ball and Chiellini tapped it into the empty net.
In the 55th minute Italy forward Eder had an golden chance for a goal in a one-on-one showdown with de Gea, but the Manchester United ‘keeper was quick to save it.
In the 90th minute Spain center back Gerard Pique was unable to benefit from a mistake in the Italian defense.
Just a minute later Italy doubled their score on the break. Southampton forward Graziano Pelle finished with a volley, securing victory for the Azzurri.
Italy will meet Germany in a quarter-final match on Saturday but will be without the services of Thiago Motta, who was suspended.